From 18ed7862de391422f632f720902be93f2e8cd0b9 Mon Sep 17 00:00:00 2001
From: Zepei Xu <xuzepei19950617@gmail.com>
Date: Tue, 14 Nov 2017 14:55:28 -0800
Subject: [PATCH] move files to right place
---
.../spec => mol-io/reader/_spec}/mol2.spec.ts | 0
src/{ => mol-io}/reader/mol2/parser.ts | 52 +++++++++----------
2 files changed, 26 insertions(+), 26 deletions(-)
rename src/{reader/spec => mol-io/reader/_spec}/mol2.spec.ts (100%)
rename src/{ => mol-io}/reader/mol2/parser.ts (76%)
diff --git a/src/reader/spec/mol2.spec.ts b/src/mol-io/reader/_spec/mol2.spec.ts
similarity index 100%
rename from src/reader/spec/mol2.spec.ts
rename to src/mol-io/reader/_spec/mol2.spec.ts
diff --git a/src/reader/mol2/parser.ts b/src/mol-io/reader/mol2/parser.ts
similarity index 76%
rename from src/reader/mol2/parser.ts
rename to src/mol-io/reader/mol2/parser.ts
index 87a22cbf7..e856a87e8 100644
--- a/src/reader/mol2/parser.ts
+++ b/src/mol-io/reader/mol2/parser.ts
@@ -4,12 +4,12 @@
// but not
// const undefPooledStr = UndefinedColumn(molecule.num_atoms, ColumnType.pooledStr);
// because latter actuall return a column of zeros
+import { Column } from 'mol-data/db'
import Tokenizer from '../common/text/tokenizer'
import FixedColumn from '../common/text/column/fixed'
-import { ColumnType, UndefinedColumn } from '../common/column'
import * as Schema from './schema'
import Result from '../result'
-import Computation from '../../utils/computation'
+import Computation from 'mol-util/computation'
interface State {
tokenizer: Tokenizer,
@@ -51,7 +51,7 @@ function State(tokenizer: Tokenizer, ctx: Computation.Context): State {
function handleMolecule(state: State) {
const { tokenizer, molecule } = state;
- Tokenizer.markLine(tokenizer); // skip the line '@<TRIPOS>MOLECULE'
+ Tokenizer.markLine(tokenizer);
Tokenizer.markLine(tokenizer);
let name = Tokenizer.getTokenString(tokenizer);
molecule.mol_name = name;
@@ -111,29 +111,25 @@ async function handleAtoms(state: State): Promise<Schema.Atoms> {
}
const col = FixedColumn(lines);
- const undefInt = UndefinedColumn(molecule.num_atoms, ColumnType.int);
- const undefFloat = UndefinedColumn(molecule.num_atoms, ColumnType.float);
+ const undefInt = Column.Undefined(molecule.num_atoms, Column.Schema.int);
+ const undefFloat = Column.Undefined(molecule.num_atoms, Column.Schema.float);
//const undefPooledStr = UndefinedColumn(molecule.num_atoms, ColumnType.pooledStr);
// created below column to pass unit tests
- const undefStr = UndefinedColumn(molecule.num_atoms, ColumnType.str);
+ const undefStr = Column.Undefined(molecule.num_atoms, Column.Schema.str);
const ret = {
count: molecule.num_atoms,
- atom_id: col(0, 7, ColumnType.int),
- atom_name: col(7, 9, ColumnType.pooledStr),
- x: col(16, 10, ColumnType.float),
- y: col(26, 10, ColumnType.float),
- z: col(36, 10, ColumnType.float),
- atom_type: col(46, 6, ColumnType.pooledStr),
+ atom_id: col(0, 7, Column.Schema.int),
+ atom_name: col(7, 9, Column.Schema.str),
+ x: col(16, 10, Column.Schema.float),
+ y: col(26, 10, Column.Schema.float),
+ z: col(36, 10, Column.Schema.float),
+ atom_type: col(46, 6, Column.Schema.str),
// optional properties
- subst_id: hasSubst_id ? col(52, 6, ColumnType.int) : undefInt,
- subst_name: hasSubst_name ? col(58, 8, ColumnType.pooledStr) : undefStr,
- charge: hasCharge ? col(66, 10, ColumnType.float) : undefFloat,
- // undefPooledStr cannot pass unit tests because it create a column of zeros but not empty strings
- //status_bit: hasStatus_bit ? col(76, 100, ColumnType.pooledStr) : undefPooledStr,
-
- // use undefStr instead to pass unit tests
- status_bit: hasStatus_bit ? col(76, 100, ColumnType.pooledStr) : undefStr,
+ subst_id: hasSubst_id ? col(52, 6, Column.Schema.int) : undefInt,
+ subst_name: hasSubst_name ? col(58, 8, Column.Schema.str) : undefStr,
+ charge: hasCharge ? col(66, 10, Column.Schema.float) : undefFloat,
+ status_bit: hasStatus_bit ? col(76, 100, Column.Schema.str) : undefStr,
};
@@ -160,18 +156,22 @@ async function handleBonds(state: State): Promise<Schema.Bonds> {
const col = FixedColumn(lines);
//const undefPooledStr = UndefinedColumn(molecule.num_bonds, ColumnType.pooledStr);
// created below column to pass unit tests
- const undefStr = UndefinedColumn(molecule.num_atoms, ColumnType.str);
+ const undefStr = Column.Undefined(molecule.num_atoms, Column.Schema.str);
+
+ // if don't want to assume a fixed format, we can access a value of a column at a certain row by
+ // parse out the whole line at row x, then split the line, and return the yth value that is at the
+ // index of wanted value.
const ret = {
count: molecule.num_bonds,
- bond_id: col(0, 6, ColumnType.int),
- origin_atom_id: col(6, 6, ColumnType.int),
- target_atom_id: col(12, 6, ColumnType.int),
- bond_type: col(18, 5, ColumnType.pooledStr),
+ bond_id: col(0, 6, Column.Schema.int),
+ origin_atom_id: col(6, 6, Column.Schema.int),
+ target_atom_id: col(12, 6, Column.Schema.int),
+ bond_type: col(18, 5, Column.Schema.str),
// optional properties
// undefPooledStr cannot pass unit tests because it create a column of zeros but not empty strings
//status_bits: hasStatus_bit ? col(23, 50, ColumnType.pooledStr) : undefPooledStr,
- status_bits: hasStatus_bit ? col(23, 50, ColumnType.pooledStr) : undefStr,
+ status_bits: hasStatus_bit ? col(23, 50, Column.Schema.str) : undefStr,
};
return ret;
--
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